Version 0.8.5 New 'autobin' command, replacing the script `coverage_bin_size.py`. Fixed some bugs and usability issues. Unit tests improved, especially for the 'cnvlib.genome' sub-package. Dependencies ------------ - Pandas 0.18.1 is once again supported. Previously the minimum version was 0.19.1. (chapmanb/bcbio-nextgen#1836) - Pysam minimum version is still 0.9.1.4, but slightly older versions in the 0.9 series may still work too. (#192) Commands -------- `autobin`: - New command, replacing and extending the script `coverage_bin_size.py`. The script is still included (and shares most of the same code), but is considered deprecated and will be removed in the 0.9.0 release. (#170) - In 'amplicon' and 'hybrid' modes, ensure sampling regions for coverage is the same in every run by set random seed. (#191) `antitarget`, `autobin`, `batch`: - Fix an issue in GenomicArray.subtract() that caused some of the expected output regions to be missing. In cases where this caused an entire chromosome to be lost, the `coverage_bin_size.py` script` and autobin` and `batch` commands in `hybrid` mode would crash. (chapmanb/bcbio-nextgen#1799) `batch`, `diagram`: - Fix creation of chromosomal diagrams with `--diagram` and the `diagram` command. (#190) `export`: - In `export seg`, use 1-based indexing in the SEG output. (#197) - Fix `export cdt` format; it was generating Java TreeView (jtv) earlier.